[adegenet-forum] Nucleotide substitution model used by haploGen()/SeqTrack()

[Jarrett Phillips]

My inquiry concerns seqTrack(), which employs haploGen() to simulate a haplotype genealogy through time.

haploGen() generates DNA sequences under a Kimura-2-Parameter substitution model with equal base frequencies and differing transition/transversion rates.

My question is: how can we be certain that the sequences really do conform to a K2P model? Since these are simulated data, it would be difficult to choose the most parsimonious model based on the BIC (using MEGA software for instance), as one is required to select the appropriate codon table (e.g., standard vs. mitochondrial), to ensure proper placement of STOP codons.

Trying this approach for each of standard and mitochondrial codon tables seems to give conflicting results as to the best substitution model.


Could someone shed some light on this? I would appreciate any insight one might be able to offer.

Thanks.
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